ClinVar Miner

Submissions for variant NM_000527.5(LDLR):c.1761C>G (p.Ser587Arg)

dbSNP: rs753430282
Minimum review status: Collection method:
Minimum conflict level:
ClinVar version:
Total submissions: 7
Download table as spreadsheet
Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
LDLR-LOVD, British Heart Foundation RCV000238260 SCV000295643 uncertain significance Hypercholesterolemia, familial, 1 2016-03-25 criteria provided, single submitter literature only
Color Diagnostics, LLC DBA Color Health RCV000775076 SCV000909178 uncertain significance Familial hypercholesterolemia 2023-05-12 criteria provided, single submitter clinical testing This missense variant (also known as p.Ser566Arg in the mature protein) replaces serine with arginine at codon 587 of the LDLR protein. Computational prediction suggests that this variant may have a deleterious impact on protein structure and function (internally defined REVEL score threshold >= 0.7, PMID: 27666373). To our knowledge, functional studies have not been reported for this variant. This variant has been reported in individuals affected with familial hypercholesterolemia (PMID: 16250003, 33740630) and in an individual affected with coronary artery disease (PMID: 27050191). It has also been reported in a healthy control individual (PMID: 30586733). This variant has been identified in 4/251490 chromosomes in the general population by the Genome Aggregation Database (gnomAD). The available evidence is insufficient to determine the role of this variant in disease conclusively. Therefore, this variant is classified as a Variant of Uncertain Significance.
Ambry Genetics RCV002411089 SCV002716040 uncertain significance Cardiovascular phenotype 2022-04-13 criteria provided, single submitter clinical testing The p.S587R variant (also known as c.1761C>G), located in coding exon 12 of the LDLR gene, results from a C to G substitution at nucleotide position 1761. The serine at codon 587 is replaced by arginine, an amino acid with dissimilar properties. This alteration was detected in a hypercholesterolemia, coronary artery cohorts; however, clinical details were limited (Fouchier SW et al. Hum. Mutat., 2005 Dec;26:550-6; Khera AV et al. J. Am. Coll. Cardiol., 2016 Jun;67:2578-89; Leren TP et al. Atherosclerosis, 2021 04;322:61-66). This alteration was also detected in a control subject in a whole exome sequencing cohort (Khera AV et al. Circulation, 2019 03;139:1593-1602). This amino acid position is well conserved in available vertebrate species. In addition, this alteration is predicted to be deleterious by in silico analysis. Since supporting evidence is limited at this time, the clinical significance of this alteration remains unclear.
Invitae RCV000775076 SCV004397372 uncertain significance Familial hypercholesterolemia 2023-06-25 criteria provided, single submitter clinical testing In summary, the available evidence is currently insufficient to determine the role of this variant in disease. Therefore, it has been classified as a Variant of Uncertain Significance. Algorithms developed to predict the effect of sequence changes on RNA splicing suggest that this variant may create or strengthen a splice site. Advanced modeling of protein sequence and biophysical properties (such as structural, functional, and spatial information, amino acid conservation, physicochemical variation, residue mobility, and thermodynamic stability) performed at Invitae indicates that this missense variant is expected to disrupt LDLR protein function. ClinVar contains an entry for this variant (Variation ID: 252021). This missense change has been observed in individual(s) with familial hypercholesterolemia (PMID: 16250003, 20506408, 33740630). This variant is present in population databases (rs753430282, gnomAD 0.004%). This sequence change replaces serine, which is neutral and polar, with arginine, which is basic and polar, at codon 587 of the LDLR protein (p.Ser587Arg).
All of Us Research Program, National Institutes of Health RCV000238260 SCV004822495 uncertain significance Hypercholesterolemia, familial, 1 2023-10-06 criteria provided, single submitter clinical testing This missense variant (also known as p.Ser566Arg in the mature protein) replaces serine with arginine at codon 587 of the LDLR protein. Computational prediction suggests that this variant may have a deleterious impact on protein structure and function (internally defined REVEL score threshold >= 0.7, PMID: 27666373). To our knowledge, functional studies have not been reported for this variant. This variant has been reported in individuals affected with familial hypercholesterolemia (PMID: 16250003, 33740630) and in an individual affected with coronary artery disease (PMID: 27050191). It has also been reported in a healthy control individual (PMID: 30586733). This variant has been identified in 4/251490 chromosomes in the general population by the Genome Aggregation Database (gnomAD). The available evidence is insufficient to determine the role of this variant in disease conclusively. Therefore, this variant is classified as a Variant of Uncertain Significance.
Laboratorium voor Moleculaire Diagnostiek Experimentele Vasculaire Geneeskunde, Academisch Medisch Centrum RCV000238260 SCV000606507 pathogenic Hypercholesterolemia, familial, 1 no assertion criteria provided research
GenomeConnect, ClinGen RCV000238260 SCV000607061 not provided Hypercholesterolemia, familial, 1 no assertion provided phenotyping only GenomeConnect assertions are reported exactly as they appear on the patient-provided report from the testing laboratory. GenomeConnect staff make no attempt to reinterpret the clinical significance of the variant.

The information on this website is not intended for direct diagnostic use or medical decision-making without review by a genetics professional. Individuals should not change their health behavior solely on the basis of information contained on this website. Neither the University of Utah nor the National Institutes of Health independently verfies the submitted information. If you have questions about the information contained on this website, please see a health care professional.